https://github.com/Sage-Bionetworks/prov-service
lightweight implementation of the Synapse Activity services, based on the PROV spec
https://github.com/Sage-Bionetworks/prov-service
Last synced: 19 days ago
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lightweight implementation of the Synapse Activity services, based on the PROV spec
- Host: GitHub
- URL: https://github.com/Sage-Bionetworks/prov-service
- Owner: Sage-Bionetworks
- Created: 2019-04-02T19:54:12.000Z (about 6 years ago)
- Default Branch: develop
- Last Pushed: 2023-02-15T23:43:07.000Z (over 2 years ago)
- Last Synced: 2024-04-23T13:37:34.997Z (about 1 year ago)
- Language: Python
- Size: 1.32 MB
- Stars: 3
- Watchers: 9
- Forks: 3
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
- awesome-synapse - prov-service - lightweight implementation of the Synapse Activity services, based on the PROV spec (Python / Shiny)
README
# Provenance Service
`develop` branch status: [](https://travis-ci.com/Sage-Bionetworks/prov-service) [](https://coveralls.io/github/Sage-Bionetworks/prov-service?branch=master&service=github)
Lightweight implementation of the Synapse Activity services, based on the PROV spec.
## Overview
This is an OpenAPI-enabled (and documented) Flask server. This example uses the [Connexion](https://github.com/zalando/connexion) library on top of Flask. The [py2neo]() driver library for Python is used to manage operations between RESTful API requests/responses and a Neo4j database.
This server was originally generated by the [OpenAPI Generator](https://openapi-generator.tech) project. Starting with the Synapse Activity API specification in a `swagger.yaml` file, the contents of this repo were originally generated with the following command:
```shell
npx openapi-generator generate -i swagger.yaml -g python-flask -DpackageName=synprov -o prov-service/
```
## Requirements
Python 3.6
You should have access to a local installation of Neo4j, serving at `bolt://localhost/7687`*.
You'll also need to set two environment variables based on your Neo4j configuration (the Flask app uses these to connect to the database):
```shell
export NEO4J_USERNAME= # must be 'neo4j'
export NEO4J_PASSWORD=
```
*In some cases, the **Neo4j Desktop** app decides to serve the database on port `11001` instead of `7687`. If this happens, you can set an additional environment variable:
```shell
export NEO4J_PORT=11001
```
## Usage
To run the server, please execute the following from the root directory:
```shell
pip install -r requirements.txt .
```
To start the app, you can use this command:
```shell
synprov
```
To initialize the graph database with mock activity records, you can run the app with additional parameters:
```shell
synprov --mock_db --db_size 30
```
To view the full set of parameters:
```shell
synprov --help
```
```shell
Usage: synprov [OPTIONS]
Options:
--mock_db Initialize Neo4j database with mock graph records
[default: False]
--db_size INTEGER Number of mock activity records to create in the graph
database (ignored if 'init_db' is False). [default: 50]
--help Show this message and exit.
```
### Neo4j browser
If you have the **Neo4j Desktop** application installed, you should be able to view and explore the graph database using Cypher queries. For example, to view all nodes and relationships:
```cypher
MATCH (n) RETURN n
```
Assuming that you populated the graph database with mock/example records as described above, you should see something that looks like this (minus the custom colors):
### Swagger UI
You can also interact with the graph database through RESTful API queries. The service provides a Swagger UI endpoint to test requests through the browser:
```
http://localhost:8080/rest/ui/
```
*If the above URL doesn't work, try this instead:*
```
http://0.0.0.0:8080/rest/ui/
```
The OpenAPI definition lives here:
```
http://localhost:8080/rest/openapi.json
```
## Running with Docker
To run the server on a Docker container, execute the following from the root directory:
```shell
docker-compose up --build
```
> **Note:** In order to use the server container, which requires a Neo4j database connection, you should have [Docker Compose](https://docs.docker.com/compose/overview/) installed.
After running this command, the URLs in the previous section should work.
## Development
To add changes locally, install the package in developer mode:
```shell
pip install -r requirements.txt -e .
```
### OpenAPI Generator
The core `models` and `controllers` for the server are generated automatically from the OpenAPI specification. Classses and methods used for operations within the app all inherit from auto-generated definitions.
Anytime the OpenAPI spec is modified, controller and model code should be regenerated with the following command:
```shell
npx openapi-generator generate \
-c .openapi-generator-config \
-t .codegen/server \
-Dmodels \
-DmodelTests=false \
-Dapis \
-DapiTests=false \
-i synprov/openapi/openapi.yaml \
-g python-flask \
-o .
```
**Note:** this will happen during the continuous integration process regardless, so regenerating and testing locally is just advised to save time troubleshooting.